Variant rs753420 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.303 in 212,566 control chromosomes in the GnomAD database, including 10,591 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.29 ( 7066 hom., cov: 32)

Exomes 𝑓: 0.33 ( 3525 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0590

Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.64 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.294

AC:

44606

AN:

151976

Hom.:

7052

Cov.:

show subpopulations

Gnomad AFR

AF:

0.267

Gnomad AMI

AF:

0.182

Gnomad AMR

AF:

0.355

Gnomad ASJ

AF:

0.278

Gnomad EAS

AF:

0.659

Gnomad SAS

AF:

0.351

Gnomad FIN

AF:

0.257

Gnomad MID

AF:

0.342

Gnomad NFE

AF:

0.271

Gnomad OTH

AF:

0.307

GnomAD4 exome

AF:

0.326

AC:

19703

AN:

60472

Hom.:

3525

Cov.:

AF XY:

0.324

AC XY:

9807

AN XY:

30266

show subpopulations

Gnomad4 AFR exome

AF:

0.277

Gnomad4 AMR exome

AF:

0.413

Gnomad4 ASJ exome

AF:

0.297

Gnomad4 EAS exome

AF:

0.659

Gnomad4 SAS exome

AF:

0.414

Gnomad4 FIN exome

AF:

0.284

Gnomad4 NFE exome

AF:

0.286

Gnomad4 OTH exome

AF:

0.316

GnomAD4 genome

AF:

0.294

AC:

44663

AN:

152094

Hom.:

7066

Cov.:

AF XY:

0.296

AC XY:

22007

AN XY:

74342

show subpopulations

Gnomad4 AFR

AF:

0.268

Gnomad4 AMR

AF:

0.355

Gnomad4 ASJ

AF:

0.278

Gnomad4 EAS

AF:

0.659

Gnomad4 SAS

AF:

0.352

Gnomad4 FIN

AF:

0.257

Gnomad4 NFE

AF:

0.271

Gnomad4 OTH

AF:

0.309

Alfa

AF:

0.280

Hom.:

10217

Bravo

AF:

0.303

Asia WGS

AF:

0.494

AC:

1717

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

4.1

DANN

Benign

0.49

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over